|
| Status |
Public on Nov 15, 2014 |
| Title |
Induced beta cell 7m |
| Sample type |
SRA |
| |
|
| Source name |
Induced beta cell
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype/variation: Rag1-/-
tissue: Pancreas
tissue/cell type: Cherry+ induced beta cells
samples collected at: 7 months
|
| Treatment protocol |
Pancreata were perfused through the common bile duct. After removing endogenous islets, the acinar fraction was digested with liberase and Elastase (Roche) into single cells.
|
| Growth protocol |
Rag1-/- were obtained from Jackson Labs (http://jaxmice.jax.org/strain/002216.html). For β- cell induction, 100ul (>1x 10^9 pfu) of purified adenovirus was directly injected into the splenic lobe of the dorsal pancreas.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cherry+ induced beta cells were isolated by fluorescent activated cell sorting (FACS) with FACSaria (BD Bioscience), RNA samples were extracted by Trizol
mRRBS libraries were prepared as previously described (Boyle et al. 2012). Briefly, genomic sequences were digested using the MspI restriction enzyme, which cuts at the sequence CCGG. Digested fragments were subjected to bisulfite treatment which converts unmethylated cytosine residues to uracil
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
7M.meth
|
| Data processing |
Alignment: bisulfite-converted reads were aligned to a MspI-digested mm9 mouse genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain methylation information for each CpG covered by mRRBS. For each CpG, the methylation is shown as the number of times the CpG was methylated over the total times the CpG was measured.
|
| |
|
| Submission date |
Jul 21, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kendell Clement |
| Organization name |
Harvard University
|
| Lab |
Meissner Lab
|
| Street address |
7 Divinity Ave.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE59615 |
Transcriptional and epigenetic program changes of induced beta cells over time [RRBS-seq] |
|
| Relations |
| BioSample |
SAMN02928569 |
| SRA |
SRX658102 |
